Lewin was reportedly stabbed aboard American Airlines Flight 11 as it was hijacked during the September 11 attacks. A 2001 FAA memo suggests he may have been shot by Satam al-Suqami after he attempted to foil the hijacking.[8][9] According to the FAA, Lewin was seated in business class in seat 9B, close to hijackers Mohamed Atta, Abdulaziz al-Omari and al Suqami (who was possibly seated behind him). It was first reported that he had been shot by al Suqami, although this assertion was later changed to a stabbing. According to the 9/11 Commission, Lewin was stabbed by one of the hijackers, probably Satam al Suqami, who was seated directly behind him. The commission speculates that this may have occurred during an attempt by Lewin to confront one of the hijackers in front of him, not realizing that al Suqami was sitting just behind him.[10] Lewin was identified as the first victim of the September 11 attacks.[2][11][3]

Lewin is survived by his wife Anne and his two sons, Eitan and Itamar, who were aged five and eight at the time of the September 2001 attacks.[4][5][12]

After his death, the intersection of Main and Vassar Streets in Cambridge, Massachusetts, was renamed Danny Lewin Square in his honor.[12] The award given to the best student-authored paper at the ACM Symposium on Theory of Computing (STOC) was also named the Danny Lewin Best Student Paper Award, in his honor.[6] In 2011, on the tenth anniversary of his death, Lewin's lasting contributions to the Internet were memorialized by friends and colleagues who knew him.[13][14]